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GrotjahnLab / surface_morphometrics

Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.
GNU General Public License v3.0
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Adjust scaling so that all surfaces are scaled as desired #3

Closed bbarad closed 2 years ago

bbarad commented 2 years ago

Currently, surfaces are rescaled to nanometer scaling during pycurv operation. It is essential to make sure that all of our surfaces are both scaled and origined to the original label file from day one to simplify transformation. This is going to be a multistep fix, but I need to do the following:

  1. Add a user-adjustable nm/Å switch - for math purposes, doing everything in nm is much simpler (and matches the Pycurv convention), but obviously it should be up to users!
  2. Adjust point cloud generation to be scaled to the correct voxel size, scaled to nm/Å
  3. Adjust the masking operation during mesh-making to be voxel-size sensitive, scaled to nm/Å
  4. Stop rescaling at pycurv time - assume scale is correct but use voxel size to correctly mask back edge voxels for calculations. Need an nm/Å switch here too.

After pycurv, all calculations should be unaffected - the VTP, TG, and CSV outputs should all be self-consistent and scaled to nm (I will need to add some labeling to note if they are in Å mode).

bbarad commented 2 years ago

This is complete with the most recent pull request!